Amplicon-Based Next Generation Sequencing for Rapid Identification of and Ectoparasite Species from Entomological Surveillance in Thailand.

Background: Next generation sequencing (NGS) technology has been used for a wide range of epidemiological and surveillance studies. Here, we used amplicon-based NGS to species identify and their arthropod hosts from entomological surveillance.

Methods: During 2015-2016, we screened 1825 samples of rodents and ectoparasites collected from rodents and domestic mammals (dog, cat, and cattle) across Thailand for . The citrate synthase gene was amplified to identify to species, while the Cytochrome Oxidase subunit I (I) and subunit II (II) genes were used as target genes for ectoparasite identification. All target gene amplicons were pooled for library preparation and sequenced with Illumina MiSeq platform.

Result: The highest percentage of DNA was observed in fleas collected from domestic animals (56%) predominantly dogs. Only a few samples of ticks from domestic animals, rodent fleas, and rodent tissue were positive for DNA. NGS based characterization of by host identified as the most common bacteria in positive fleas collected from dogs (83.2%) while " Rickettsia senegalensis" was detected in only 16.8% of positive dog fleas. Sequence analysis of I and II revealed that almost all fleas collected from dogs were . Other species were detected by NGS including from two ticks, and in two rodent tissue samples.

Conclusion: This study demonstrates the utility of NGS for high-throughput sequencing in the species characterization/identification of bacteria and ectoparasite for entomological surveillance of rickettsiae. A high percentage of are positive for . In addition, our findings indicate there is a risk of tick-borne Spotted Fever Group rickettsiosis, and flea-borne murine typhus transmission in Tak and Phangnga provinces of Thailand.